One Mission at a Time
by Altonish
Summary: Last night Chuck uploaded the new Intersect. Chuck is worried that Bryce's death will hit Sarah the hardest. He is determined to comfort her, but Sarah's tears are not for Bryce. One possible beginning to season three... Season 2 spoilers everywhere!


_**Disclaimer:**_ _I don't own Chuck. If I did own Chuck, he wouldn't end up in these ridiculous situations. He'd end up in totally different ridiculous situations. _

**One Mission at a time**

Chuck was worried. He didn't know what to think. Sarah hadn't shown up for the briefing with General Beckman. She'd barely said two words to him last night when they'd parted. It was obvious that she had been deeply affected by Bryce's death. He couldn't blame her. He himself wasn't doing particularly well with the information. His best friend from college, the person who'd pushed him and manipulated him for most of his adult life was dead, again. It didn't hurt as much as he expected, but it certainly troubled him. Whatever the result of Bryce's actions had been, he'd made the best choices he could. Bryce had said it himself. He'd sent Chuck the Intersect because he knew he could handle it and because he knew Sarah would find him…

She had found him. Sarah had not only tracked down the computer nerd, the Stanford drop out that lived with his sister and was wasting his life at the Buy More, but she'd reached inside him and found something more. Regardless of the confusion her feelings provided, she'd changed him. She changed him so much that he now willingly bore the brunt of the curse he'd been trying to escape for almost two years.

Now he owed Sarah. What exactly he owed her he couldn't be sure, but he had to find some way to help her. He had to find a way to make Bryce's death less horrible for her. He didn't even know if he'd even get the chance. Sarah was supposed to be leaving this morning and at their briefing earlier General Beckman had been vague as to the future of Operation Bartowski.

Chuck knocked on the green door hoping his words wouldn't fail him. If ever he needed to be the eloquent schnook, now was the time. Unfortunately, there was no response to his knock. Apparently, wherever she was, this wasn't it, or perhaps she'd fallen asleep and he was waking her…

He'd given up and was almost back to the elevator when he heard the door unlatch and heard her call his name. "Chuck" It was quiet, but in the near silence of the hallway it rang like a church bell.

Chuck spun around and walked quickly back to her door. She was peeking out from the crack in the doorway. Sarah was still dressed in her clothes from the mission last night. Her eyes were red and her face was puffy, she looked terrible. "Hi," Chuck whispered.

"Hi," she replied in a barely audible voice.

"I uh…" Chuck started. His thoughts tumbled in on him as he tried to explain why he was here. So many reasons…so much doubt. "I was worried about you," Chuck finally admitted.

"Me?" Sarah asked.

"Yeah, well you didn't show up for the mission briefing with Beckman."

"Oh."

Chuck took a deep breath. "Can I come in?"

Sarah nodded slowly and turned to walk away from the door. She didn't open it for him, she only stopped blocking his path and when he pushed the door open she was sitting in the exact center of her bed, her chin resting on her knees and her arms wrapped around her legs. The only sign that anybody had been in this apartment all night were her boots discarded at the foot of the bed. Unsure of where to sit, Chuck finally decided to lean against her vanity so that he could look at her and she would be looking at him. Sarah, however, wasn't looking at him; she was looking through him and seemed a million miles away.

Chuck let her stay like that for a while before he finally said. "I'm really sorry about Bryce." Sarah only shrugged in reply. Chuck sighed, he wanted to wrap her up in a hug and comfort her, but it was too hard to tell how Sarah would take that. Infringing on the personal boundaries of an assassin was just dumb. "It'll be okay," Chuck finally offered. "I'm kind of shocked about Bryce too. He was my best friend for four years and sometimes it seems like I hardly knew the guy."

Sarah's eyes flickered to his briefly, before she resumed her stare through him, through the wall and back to whatever she was watching that apparently only she could see.

"Beckman wants to talk to you," Chuck tried. He got a slow nod in response, but Sarah's stare didn't break. Chuck got on his knees at the foot of Sarah's bed putting his face directly in her line of vision. "Talk to me Sarah…let me help."

Sarah shook her head slowly. "Why?"

"Because I care about you and you're scaring me," Chuck replied.

"No." Sarah closed her eyes for a moment before she opened them and looked straight at him, two pools of deep blue pain searched his face. There was something else there…anger? "Why did you do it? Why did you upload it?"

"_Oh… _I uh…didn't want to just destroy it and I couldn't let whoever those guys were get it. So I did the only thing I could think of."

"They could have just taken you, instead. Did you think of that?"

Chuck nodded slowly. "I trusted you not to let that happen. "

"_I _was captured, they could have killed all of us. You were supposed to be getting help."

"Well I did help…" Chuck grinned. "Afterwards admittedly, but it worked…"

"This isn't a joke!" Sarah replied angrily.

"Two years! Two years we tried to find some way to remove the Intersect. It was all you cared about, all you wanted. I spent two years of my life trying to do that for you. We finally do it, we finally find some way and one day later you upload the God damn thing again!"

"Sarah…" Chuck sat back, stunned at the venom in Sarah's voice. "It was the only thing I could think of!"

"You couldn't think of just not uploading it? Just destroying the damn thing and getting the hell out of there?"

"I was trapped! I came in through a ceiling vent, there was no chance I could get back out that way."

"So you just decided to let those other spies have you."

"No, we'd think of something. We always think of something." Sarah closed her eyes and shook her head. Chuck slowly stood up and sat down next to her. He reached out an arm and put it around her but she jumped when he touched her. She immediately shrugged off his hand and scooted out of his reach.

"Sarah, why are you angry with me? I couldn't have saved Bryce. I wanted too, but he only lasted a minute or two before…"

"Shut up," Sarah said angrily. Chuck looked at her. He was so confused by Sarah's actions and he had to admit that it hurt that she wouldn't let him comfort her. "I'm sorry about Bryce too," she finally said. "But what really hurts is that you killed us."

"What?" Chuck asked.

"Us, you and I, I thought you'd want to be with me and then you go and stick that stupid computer back in your brain!"

"Sarah, I…" Chuck had no idea what to say to that. "What, us? You said you were leaving this morning. If anything, this maybe saved us…because I'm assuming the NSA won't want to leave me alone now…"

"I wasn't going to go!" Sarah shouted back angrily. "I tried to tell you last night. I don't want to save the world anymore. I just wanted to be the girl you chose to spend your life with." Chuck reached out for Sarah again, but she slapped his hand away. "But you chose to be the Intersect instead."

"That's what Bryce meant." Chuck grabbed a fistful of his hair. "That makes so much more sense now."

"What?"

"Right before Bryce died, he told me that you weren't coming with him. It didn't make any sense because you'd told me just this morning that you were leaving. So, I couldn't figure out what he meant. I thought maybe you'd decided to go somewhere else…"

"I was going to stay," Sarah explained slowly. "I hadn't told General Beckman yet, but ever since yesterday morning when she told me I had to leave… I didn't want to, I couldn't, I tried…" Sarah sighed. "I can't just walk away from you."

Chuck grinned. "Well, that's great then." Chuck reached out for her once more and was once again rebuffed.

"No, it's not. We're right back where we were two days ago. You have the Intersect in your head and I'm a CIA operative. Just like I told you the last time we almost had something more…as long as the Intersect is still in there," She pointed to his forehead. "It's inappropriate. It's actually worse now."

"Worse…Sarah, I love you, I'll do whatever it takes to make this work…"

Sarah gave him a sad smile. "I know you would," She reached out and stroked his face, the first time she'd touched him since he'd arrived in her apartment. "but at best you're an asset and I'm your handler. At worst, I'm your boss and you're my employee. Anything we had would be classified as fraternization…technically, we aren't even supposed to spend time together as friends."

Chuck closed his eyes as wave after wave of disappointment washed over him. "So you're saying we can't be together?"

"I'm sorry," Sarah answered. The words hit him like a stab to the heart.

"We can get the Intersect back out again…"

"General Beckman won't want to do that, at least not until they can put it in someone else."

Chuck opened his eyes and stared at Sarah. "But what about us?"

"As long as you're the Intersect, _us, _can only be a cover."

"And after?" Chuck asked.

"One mission at a time, Chuck. One mission at a time."


End file.
